Upland and marginal farmers will benefit most from £160m of backdated subsidy for the agriculture sector.
The money is the first half of EU convergence funding which was meant to increase support levels in Scotland but was instead distributed across the UK.
Scottish ministers insist the new allocation adheres to the spirit of where the original money was intended.
But NFU Scotland said the funding allocation is a "missed opportunity" which is just plugging a funding gap.
The chancellor agreed in September to finally hand over the funds but it is up to the Scottish government to decide how it is distributed.
All basic payments will be topped up but those with the largest amount of "less favoured" land will receive the most.
Some money will also be distributed through incentives like the suckler beef support scheme.
Rural Economy Secretary Fergus Ewing said: "I believe this approach gets the money to where it needs to be and will result in all eligible farmers and crofters either increasing or significantly increasing the money in their bank accounts.
"I have given careful consideration in deciding this approach and would like to thank everyone for their support and suggestions on how best to fairly allocate this money over the last couple of weeks."
NFU Scotland's president, Andrew McCornick, added: "It is important to say from the outset that we absolutely believe that Scottish farmers and crofters should have seen the full payment made in a single year rather than spread over two.
"In addition, we cannot agree with Scottish government's proposition to use any of the £160m pot to address the budget shortfall that has been created in the Less Favoured Area Support Scheme (LFASS) in 2019 or 2020.
"To strip this money from the £160m to fill the hole in the LFASS budget is a missed opportunity and a blow to beleaguered Scottish farmers and crofters."
The convergence uplift was meant to increase subsidies for those areas which were well below the EU average.
The UK qualified for £190m because of low funding levels in Scotland but only £30m was distributed north of the border.
Farming leaders and politicians have spent years trying to convince the UK government that Scotland was short-changed.
Speyside livestock farmer Robert Macdonald said the money would be a welcome boost at a time the industry was struggling.
He added: "Some will use it to invest in their holdings, others will use it to draw down debt which is an increasing problem in the industry.
"It's money that we have been due since 2015 and money which has been lost to the industry in that time."